exporting PCA meshes in geomorph

Sergio Almécija

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Aug 18, 2017, 8:06:27 AM8/18/17

to geomorph R package

Hi all,

I would appreciate some guidance regarding a little technical problem I am encountering with geomorph when exporting the warped meshes using the command ‘writePLY’ from rgl:

A couple of years ago when I first tried the function ‘plotTangentSpace’ in my computer, it would produce different rgl windows for the negative and positive extremes along the axis. Then I would export the meshes independently (to use in my figures) using ‘writePLY’. However, now I found out that the ‘plotTangentSpace’ function would give me both extremes in the same rgl window. This is very cool and facilitates comparisons, but when attempting to export the meshes using ‘writePLY’ only the second mesh (positive extreme) is exported. I don’t know if this is related to be using a newer version of geomorph or rgl and I cannot find a way to directly export the negative axis.

Any advice would much appreciate it!

Thank you very much,

Sergio Almécija

Adams, Dean [EEOBS]

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Aug 18, 2017, 12:32:01 PM8/18/17

to Sergio Almécija, geomorph R package

Sergio,

Please see the man page that describes use of that function. The output object for the function contains the shapes as the extremes of every PC axis in $pc.shapes

You can then use plotRefToTarget to plot the TPS grid for any of these relative to a reference shape: reference shape found using mshape().

Dean

Dr. Dean C. Adams

Professor

Department of Ecology, Evolution, and Organismal Biology

Department of Statistics

Iowa State University

www.public.iastate.edu/~dcadams/

phone: 515-294-3834

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Sergio Almécija

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Aug 18, 2017, 2:02:56 PM8/18/17

to geomorph R package

Thanks for the quick answer Dean.

I had tried this and it worked fine for all the methods ('TPS', 'vector', 'points') but not with 'surface'.

When attempting the latter option, after the 'warping mesh' message reaches 100% the console prints a long list of numbers preceded by commas and in brackets (vertices of the mesh?, see below).

What am I missing?

Sergio

'plotRefToTarget(average.extant, PCs.extant$pc.shapes$PC1min, mesh = average.mesh.extant, method = "surface")'

....[,25791] [,25792] [,25793] [,25794] [,25795] [,25796] [,25797] [,25798] [,25799] [,25800] [,25801] [,25802] [,25803] [,25804]

[,25805] [,25806] [,25807] [,25808] [,25809] [,25810] [,25811] [,25812] [,25813] [,25814] [,25815] [,25816] [,25817] [,25818]

[,25819] [,25820] [,25821] [,25822] [,25823] [,25824] [,25825] [,25826] [,25827] [,25828] [,25829] [,25830] [,25831] [,25832]

[,25833] [,25834] [,25835] [,25836] [,25837] [,25838] [,25839] [,25840] [,25841] [,25842] [,25843] [,25844] [,25845] [,25846]

[,25847] [,25848] [,25849] [,25850] [,25851] [,25852] [,25853] [,25854] [,25855] [,25856] [,25857] [,25858] [,25859] [,25860]

[,25861] [,25862] [,25863] [,25864] [,25865] [,25866] [,25867] [,25868] [,25869] [,25870] [,25871] [,25872] [,25873] [,25874]

[,25875] [,25876] [,25877] [,25878] [,25879] [,25880] [,25881] [,25882] [,25883] [,25884] [,25885] [,25886] [,25887] [,25888]

[,25889] [,25890] [,25891] [,25892] [,25893] [,25894] [,25895] [,25896] [,25897] [,25898] [,25899] [,25900] [,25901] [,25902]

[,25903] [,25904] [,25905] [,25906] [,25907] [,25908] [,25909] [,25910] [,25911] [,25912] [,25913] [,25914] [,25915] [,25916]

[,25917] [,25918] [,25919] [,25920] [,25921] [,25922] [,25923] [,25924] [,25925] [,25926] [,25927] [,25928] [,25929] [,25930]

[,25931] [,25932] [,25933] [,25934] [,25935] [,25936] [,25937] [,25938] [,25939] [,25940] [,25941] [,25942] [,25943] [,25944]

[,25945] [,25946] [,25947] [,25948] [,25949] [,25950] [,25951] [,25952] [,25953] [,25954] [,25955] [,25956] [,25957] [,25958]

[,25959] [,25960] [,25961] [,25962] [,25963] [,25964] [,25965] [,25966] [,25967] [,25968] [,25969] [,25970] [,25971] [,25972]

[,25973] [,25974] [,25975] [,25976] [,25977] [,25978] [,25979] [,25980] [,25981] [,25982] [,25983] [,25984] [,25985] [,25986]

[,25987] [,25988] [,25989] [,25990] [,25991] [,25992] [,25993] [,25994] [,25995] [,25996] [,25997] [,25998] [,25999] [,26000]

[,26001] [,26002] [,26003] [,26004] [,26005] [,26006] [,26007] [,26008] [,26009] [,26010] [,26011] [,26012] [,26013] [,26014]

[,26015] [,26016] [,26017] [,26018] [,26019] [,26020] [,26021] [,26022] [,26023] [,26024] [,26025] [,26026] [,26027] [,26028]

[,26029] [,26030] [,26031] [,26032] [,26033] [,26034] [,26035] [,26036] [,26037] [,26038] [,26039] [,26040] [,26041] [,26042]

[,26043] [,26044] [,26045] [,26046] [,26047] [,26048] [,26049] [,26050] [,26051] [,26052] [,26053] [,26054] [,26055] [,26056]

[,26057] [,26058] [,26059] [,26060] [,26061] [,26062] [,26063] [,26064] [,26065] [,26066] [,26067] [,26068] [,26069] [,26070]

[,26071] [,26072] [,26073] [,26074] [,26075] [,26076] [,26077] [,26078] [,26079] [,26080] [,26081] [,26082] [,26083] [,26084]

[,26085] [,26086] [,26087] [,26088] [,26089] [,26090] [,26091] [,26092] [,26093] [,26094] [,26095] [,26096] [,26097]

[,26098] [,26099] [,26100] [,26101] [,26102] [,26103] [,26104] [,26105] [,26106] [,26107] [,26108] [,26109] [,26110]

[,26111] [,26112] [,26113] [,26114] [,26115] [,26116] [,26117] [,26118] [,26119] [,26120] [,26121] [,26122] [,26123]

[,26124] [,26125] [,26126] [,26127] [,26128] [,26129] [,26130] [,26131] [,26132] [,26133] [,26134] [,26135] [,26136] [,26137]

[,26138] [,26139] [,26140] [,26141] [,26142] [,26143] [,26144] [,26145] [,26146] [,26147] [,26148] [,26149] [,26150] [,26151] [,26152]

[,26153]

[ reached getOption("max.print") -- omitted 4 rows ]

attr(,"class")

[1] "mesh3d" "shape3d"

>'

Sergio Almécija

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Aug 18, 2017, 3:24:37 PM8/18/17

to geomorph R package

ps. I just restarted R and now the rgl window with the warped 3D mesh appears on it. So problem solved, thanks so much!